I normally save cell source code in .eps for paper and book publishing,
process in Adobe Illustrator and include in
TeX or LaTeX as figures. See examples in
http://caswww.colorado.edu/courses.d/IFEM.d/Home.html
-> chapter notes.
Usually publishers have no problems with those .eps files if
I substitute all Mathematica-specific fonts by equivalent
standard ones. For example I replace (with Illustrator) all
Mathematica greek symbols by Symbol, which is standard
over most of this planet. I began doing that when I noticed wrong
symbols in printing of class notes by students or in publisher proofs
(if a font is missing, often a system will replace that by Courier, but
if it is a greek letter that can be completely wrong)
If you have complete control over your documents,
font replacement is not that crucial.